Added a StandardVariantContextInputArgumentCollection that is now used for consistency by many of the core tools.
This commit is contained in:
Eric Banks
parent
bc125f104a
commit
06cdc4d5f9
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@ -0,0 +1,55 @@
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.arguments;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.simpleframework.xml.Root;
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/**
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* @author ebanks
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* @version 1.0
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*/
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@Root
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public class StandardVariantContextInputArgumentCollection {
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/**
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* The VCF input file(s)
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*
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* The variant track can take any number of arguments on the command line. Each -V argument
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* will be included as an input to the tool. If no explicit name is provided,
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* the -V arguments will be named using the default algorithm: variant, variant2, variant3, etc.
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* The user can override this by providing an explicit name -V:name,vcf for each -V argument,
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* and each named argument will be labeled as such in the output (i.e., set=name rather than
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* set=variant2). The order of arguments does not matter except for the naming.
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*/
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@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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}
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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@ -35,7 +36,6 @@ import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationType;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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@ -56,8 +56,7 @@ import java.util.*;
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@By(DataSource.REFERENCE)
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public class VariantAnnotator extends RodWalker<Integer, Integer> {
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@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
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public RodBinding<SnpEffFeature> snpEffFile;
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@ -142,7 +141,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
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listAnnotationsAndExit();
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// get the list of all sample names from the variant VCF input rod, if applicable
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List<String> rodName = Arrays.asList(variants.getName());
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List<String> rodName = Arrays.asList(variantCollection.variants.getName());
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Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
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// add the non-VCF sample from the command-line, if applicable
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@ -166,7 +165,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
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// note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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hInfo.addAll(engine.getVCFAnnotationDescriptions());
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for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())) ) {
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for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) {
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if ( isUniqueHeaderLine(line, hInfo) )
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hInfo.add(line);
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}
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@ -225,7 +224,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
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if ( tracker == null )
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return 0;
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Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation());
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Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
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if ( VCs.size() == 0 )
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return 0;
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@ -25,10 +25,8 @@
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package org.broadinstitute.sting.gatk.walkers.beagle;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
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@ -54,8 +52,9 @@ import static java.lang.Math.log10;
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*/
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@Requires(value={})
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public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ArgumentCollection
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protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
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public RodBinding<VariantContext> comp = RodBinding.makeUnbound(VariantContext.class);
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@ -111,7 +110,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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hInfo.add(new VCFInfoHeaderLine("AFH", 1, VCFHeaderLineType.Float, "Allele Number from Comparison ROD at this site"));
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}
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Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
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Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variantCollection.variants.getName()));
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final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
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vcfWriter.writeHeader(vcfHeader);
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@ -123,7 +122,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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return 0;
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GenomeLoc loc = context.getLocation();
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VariantContext vc_input = tracker.getFirstValue(variants, loc);
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VariantContext vc_input = tracker.getFirstValue(variantCollection.variants, loc);
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VariantContext vc_comp = tracker.getFirstValue(comp, loc);
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.beagle;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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@ -52,8 +53,8 @@ import java.util.*;
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*/
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@Requires(value={})
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public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
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@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false)
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public RodBinding<VariantContext> validation = RodBinding.makeUnbound(VariantContext.class);
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@ -98,7 +99,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
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public void initialize() {
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samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
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samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variantCollection.variants.getName()));
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beagleWriter.print("marker alleleA alleleB");
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for ( String sample : samples )
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@ -120,7 +121,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
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public Integer map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
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if( tracker != null ) {
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GenomeLoc loc = context.getLocation();
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VariantContext variant_eval = tracker.getFirstValue(variants, loc);
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VariantContext variant_eval = tracker.getFirstValue(variantCollection.variants, loc);
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VariantContext validation_eval = tracker.getFirstValue(validation, loc);
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if ( goodSite(variant_eval,validation_eval) ) {
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@ -26,13 +26,10 @@
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package org.broadinstitute.sting.gatk.walkers.filters;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.GenomeLoc;
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@ -53,8 +50,8 @@ import java.util.*;
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@Reference(window=@Window(start=-50,stop=50))
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public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
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@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ArgumentCollection
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protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@Input(fullName="mask", doc="Input ROD mask", required=false)
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public RodBinding<Feature> mask = RodBinding.makeUnbound(Feature.class);
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@ -100,7 +97,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
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private void initializeVcfWriter() {
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final List<String> inputNames = Arrays.asList(variants.getName());
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final List<String> inputNames = Arrays.asList(variantCollection.variants.getName());
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// setup the header fields
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Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
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@ -152,7 +149,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
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if ( tracker == null )
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return 0;
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Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation());
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Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
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// is there a SNP mask present?
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boolean hasMask = tracker.hasValues(mask);
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@ -24,12 +24,12 @@
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package org.broadinstitute.sting.gatk.walkers.phasing;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.datasources.sample.Sample;
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import org.broadinstitute.sting.gatk.filters.MappingQualityZeroReadFilter;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.DisjointSet;
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@ -67,8 +67,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
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*
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* All heterozygous variants found in this VCF file will be phased, where possible
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*/
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@Input(fullName="variant", shortName = "V", doc="Phase variants from this VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ArgumentCollection
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protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@Output(doc = "File to which variants should be written", required = true)
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protected VCFWriter writer = null;
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@ -175,8 +175,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
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hInfo.add(new VCFInfoHeaderLine(PHASING_INCONSISTENT_KEY, 0, VCFHeaderLineType.Flag, "Are the reads significantly haplotype-inconsistent?"));
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// todo -- fix samplesToPhase
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Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
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Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(variants.getName()).getGenotypeSamples() : samplesToPhase);
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String trackName = variantCollection.variants.getName();
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Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
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Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(trackName).getGenotypeSamples() : samplesToPhase);
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writer.writeHeader(new VCFHeader(hInfo, samples));
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}
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@ -207,7 +208,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
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PhasingStats phaseStats = new PhasingStats();
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List<VariantContext> unprocessedList = new LinkedList<VariantContext>();
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for (VariantContext vc : tracker.getValues(variants, context.getLocation())) {
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for (VariantContext vc : tracker.getValues(variantCollection.variants, context.getLocation())) {
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if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase);
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if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) {
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@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Reference;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.Window;
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import org.broadinstitute.sting.utils.SampleUtils;
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@ -64,8 +63,8 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
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* are techincally order dependent. It is strongly recommended to provide explicit names when
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* a rod priority list is provided.
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*/
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@Input(fullName = "variant", shortName = "V", doc="The VCF files to merge together", required=true)
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public List<RodBinding<VariantContext>> variantsToMerge;
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@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
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public List<RodBinding<VariantContext>> variants;
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@Output(doc="File to which variants should be written",required=true)
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protected VCFWriter vcfWriter = null;
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@ -157,7 +156,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
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// get all of the vcf rods at this locus
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// Need to provide reference bases to simpleMerge starting at current locus
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Collection<VariantContext> vcs = tracker.getValues(variantsToMerge, context.getLocation());
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Collection<VariantContext> vcs = tracker.getValues(variants, context.getLocation());
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if ( sitesOnlyVCF ) {
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vcs = VariantContextUtils.sitesOnlyVariantContexts(vcs);
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@ -28,9 +28,9 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
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import net.sf.samtools.Cigar;
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import net.sf.samtools.CigarElement;
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import net.sf.samtools.CigarOperator;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.ArgumentCollection;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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@ -50,8 +50,9 @@ import java.util.*;
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@Reference(window=@Window(start=-200,stop=200))
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@Requires(value={})
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public class LeftAlignVariants extends RodWalker<Integer, Integer> {
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@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
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public RodBinding<VariantContext> variants;
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@ArgumentCollection
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protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@Output(doc="File to which variants should be written",required=true)
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protected VCFWriter baseWriter = null;
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@ -59,10 +60,11 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
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private SortingVCFWriter writer;
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public void initialize() {
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Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
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Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
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String trackName = variantCollection.variants.getName();
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Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
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Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
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Set<VCFHeaderLine> headerLines = vcfHeaders.get(variants.getName()).getMetaData();
|
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Set<VCFHeaderLine> headerLines = vcfHeaders.get(trackName).getMetaData();
|
||||
baseWriter.writeHeader(new VCFHeader(headerLines, samples));
|
||||
|
||||
writer = new SortingVCFWriter(baseWriter, 200);
|
||||
|
|
@ -72,7 +74,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
|
|||
if ( tracker == null )
|
||||
return 0;
|
||||
|
||||
Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation());
|
||||
Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
|
||||
|
||||
int changedSites = 0;
|
||||
for ( VariantContext vc : VCs )
|
||||
|
|
|
|||
|
|
@ -29,10 +29,8 @@ import net.sf.picard.liftover.LiftOver;
|
|||
import net.sf.picard.util.Interval;
|
||||
import net.sf.samtools.SAMFileHeader;
|
||||
import net.sf.samtools.SAMFileReader;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
import org.broadinstitute.sting.commandline.Input;
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
import org.broadinstitute.sting.commandline.RodBinding;
|
||||
import org.broadinstitute.sting.commandline.*;
|
||||
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
|
|
@ -52,8 +50,9 @@ import java.util.*;
|
|||
*/
|
||||
@Requires(value={})
|
||||
public class LiftoverVariants extends RodWalker<Integer, Integer> {
|
||||
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
|
||||
public RodBinding<VariantContext> variants;
|
||||
|
||||
@ArgumentCollection
|
||||
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
|
||||
|
||||
@Output(doc="File to which variants should be written",required=true)
|
||||
protected File file = null;
|
||||
|
|
@ -88,12 +87,13 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
|
|||
throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference");
|
||||
}
|
||||
|
||||
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
|
||||
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
|
||||
String trackName = variantCollection.variants.getName();
|
||||
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
|
||||
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
|
||||
|
||||
Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
|
||||
if ( vcfHeaders.containsKey(variants.getName()) )
|
||||
metaData.addAll(vcfHeaders.get(variants.getName()).getMetaData());
|
||||
if ( vcfHeaders.containsKey(trackName) )
|
||||
metaData.addAll(vcfHeaders.get(trackName).getMetaData());
|
||||
if ( RECORD_ORIGINAL_LOCATION ) {
|
||||
metaData.add(new VCFInfoHeaderLine("OriginalChr", 1, VCFHeaderLineType.String, "Original contig name for the record"));
|
||||
metaData.add(new VCFInfoHeaderLine("OriginalStart", 1, VCFHeaderLineType.Integer, "Original start position for the record"));
|
||||
|
|
@ -146,7 +146,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
|
|||
if ( tracker == null )
|
||||
return 0;
|
||||
|
||||
Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation());
|
||||
Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
|
||||
for ( VariantContext vc : VCs )
|
||||
convertAndWrite(vc, ref);
|
||||
|
||||
|
|
|
|||
|
|
@ -25,6 +25,7 @@
|
|||
package org.broadinstitute.sting.gatk.walkers.variantutils;
|
||||
|
||||
import org.broadinstitute.sting.commandline.*;
|
||||
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
|
||||
import org.broadinstitute.sting.utils.MathUtils;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.*;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
|
@ -61,8 +62,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
|
|||
* Variants from this file are sent through the filtering and modifying routines as directed
|
||||
* by the arguments to SelectVariants, and finally are emitted.
|
||||
*/
|
||||
@Input(fullName="variant", shortName = "V", doc="Select variants from this VCF file", required=true)
|
||||
public RodBinding<VariantContext> variants;
|
||||
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
|
||||
|
||||
/**
|
||||
* If provided, we will filter out variants that are "discordant" to the variants in this file
|
||||
|
|
@ -194,7 +194,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
|
|||
*/
|
||||
public void initialize() {
|
||||
// Get list of samples to include in the output
|
||||
List<String> rodNames = Arrays.asList(variants.getName());
|
||||
List<String> rodNames = Arrays.asList(variantCollection.variants.getName());
|
||||
|
||||
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
|
||||
TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
|
||||
|
|
@ -318,7 +318,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
|
|||
if ( tracker == null )
|
||||
return 0;
|
||||
|
||||
Collection<VariantContext> vcs = tracker.getValues(variants, context.getLocation());
|
||||
Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
|
||||
|
||||
if ( vcs == null || vcs.size() == 0) {
|
||||
return 0;
|
||||
|
|
|
|||
|
|
@ -28,13 +28,10 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
|
|||
import org.broad.tribble.Feature;
|
||||
import org.broad.tribble.TribbleException;
|
||||
import org.broad.tribble.dbsnp.DbSNPFeature;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
import org.broadinstitute.sting.commandline.Hidden;
|
||||
import org.broadinstitute.sting.commandline.Input;
|
||||
import org.broadinstitute.sting.commandline.RodBinding;
|
||||
import org.broadinstitute.sting.commandline.*;
|
||||
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
|
||||
import org.broadinstitute.sting.gatk.walkers.*;
|
||||
|
|
@ -56,8 +53,8 @@ import java.util.Set;
|
|||
@Requires(value={})
|
||||
public class ValidateVariants extends RodWalker<Integer, Integer> {
|
||||
|
||||
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
|
||||
public RodBinding<VariantContext> variants;
|
||||
@ArgumentCollection
|
||||
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
|
||||
|
||||
public enum ValidationType {
|
||||
ALL, REF, IDS, ALLELES, CHR_COUNTS
|
||||
|
|
@ -78,14 +75,14 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
|
|||
private File file = null;
|
||||
|
||||
public void initialize() {
|
||||
file = new File(variants.getSource());
|
||||
file = new File(variantCollection.variants.getSource());
|
||||
}
|
||||
|
||||
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
if ( tracker == null )
|
||||
return 0;
|
||||
|
||||
Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation());
|
||||
Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
|
||||
for ( VariantContext vc : VCs )
|
||||
validate(vc, tracker, ref);
|
||||
|
||||
|
|
|
|||
|
|
@ -24,12 +24,10 @@
|
|||
|
||||
package org.broadinstitute.sting.gatk.walkers.variantutils;
|
||||
|
||||
import org.broadinstitute.sting.commandline.Input;
|
||||
import org.broadinstitute.sting.commandline.RodBinding;
|
||||
import org.broadinstitute.sting.commandline.*;
|
||||
import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
|
||||
import org.broadinstitute.sting.utils.MathUtils;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.commandline.Argument;
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
|
|
@ -48,8 +46,8 @@ import java.util.*;
|
|||
@Requires(value={})
|
||||
public class VariantsToTable extends RodWalker<Integer, Integer> {
|
||||
|
||||
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
|
||||
public RodBinding<VariantContext> variants;
|
||||
@ArgumentCollection
|
||||
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
|
||||
|
||||
@Output(doc="File to which results should be written",required=true)
|
||||
protected PrintStream out;
|
||||
|
|
@ -138,7 +136,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
|
|||
return 0;
|
||||
|
||||
if ( ++nRecords < MAX_RECORDS || MAX_RECORDS == -1 ) {
|
||||
for ( VariantContext vc : tracker.getValues(variants, context.getLocation())) {
|
||||
for ( VariantContext vc : tracker.getValues(variantCollection.variants, context.getLocation())) {
|
||||
if ( (keepMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
|
||||
List<String> vals = extractFields(vc, fieldsToTake, ALLOW_MISSING_DATA);
|
||||
out.println(Utils.join("\t", vals));
|
||||
|
|
|
|||
Loading…
Reference in New Issue